Contacts of the helix formed by residues 1169 - 1180 (chain A) in PDB entry 5JQE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS1169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1164A CYS 4.4 2.0 - - - -
1165A ALA* 4.0 27.6 + - + +
1167A ILE 4.2 0.2 - - - -
1168A ASN* 1.3 77.3 + - - +
1170A SER* 1.3 53.3 + - - +
1171A LEU 2.9 0.4 - - - -
1172A LEU* 2.6 41.0 + - + +
1173A LYS 3.9 0.7 + - - -
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Residues in contact with SER1170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168A ASN* 2.9 21.3 + - - -
1169A LYS* 1.3 77.4 - - - +
1171A LEU* 1.3 61.8 + - - +
1172A LEU 3.2 0.4 - - - -
1173A LYS* 3.5 24.7 + - - +
1174A ILE* 3.9 12.0 + - - +
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Residues in contact with LEU1171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108A ILE* 4.5 13.2 - - + +
1111A GLU* 3.6 37.9 - - + +
1112A VAL* 3.6 26.0 - - + -
1116A GLU* 5.4 0.4 - - - +
1120A PHE* 6.4 0.9 - - + -
1164A CYS* 3.9 28.3 - - + +
1167A ILE* 4.8 7.6 - - + -
1168A ASN* 3.3 39.9 - - + +
1169A LYS 2.8 0.6 + - - -
1170A SER* 1.3 78.7 - - - +
1172A LEU* 1.3 64.0 + - - +
1174A ILE* 3.5 25.3 + - + +
1175A ILE* 3.7 10.6 - - - +
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Residues in contact with LEU1172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A LYS* 3.1 51.1 - - + +
1164A CYS* 4.6 2.5 - - + +
1165A ALA* 4.4 20.9 - - + +
1168A ASN 4.3 0.6 + - - -
1169A LYS* 2.6 25.5 + - + +
1171A LEU* 1.3 71.7 - - - +
1173A LYS* 1.3 58.2 + - - +
1175A ILE* 2.9 25.9 + - + +
1176A ASN* 3.2 26.3 + - - +
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Residues in contact with LYS1173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169A LYS 3.9 1.0 + - - -
1170A SER* 3.5 19.5 + - - +
1171A LEU 3.3 0.6 - - - -
1172A LEU* 1.3 77.6 - - - +
1174A ILE* 1.3 63.0 + - + +
1176A ASN* 3.2 12.0 + - + +
1177A ASP* 2.9 58.4 + - - +
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Residues in contact with ILE1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A MET* 4.1 14.3 - - + +
1107A GLN* 3.9 43.3 - - + +
1108A ILE* 4.0 22.2 - - + -
1111A GLU* 4.6 14.4 - - + +
1170A SER 4.0 15.0 - - - +
1171A LEU* 3.6 16.4 - - + +
1172A LEU 3.2 0.4 - - - -
1173A LYS* 1.3 76.0 - - + +
1175A ILE* 1.3 62.3 + - - +
1177A ASP* 3.6 7.7 + - - +
1178A TYR* 3.3 21.7 + - - +
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Residues in contact with ILE1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A MET* 4.3 13.9 - - + -
1108A ILE* 3.9 15.7 - - + -
1157A LEU* 4.2 20.9 - - + -
1160A LEU* 3.7 34.5 - - + +
1161A LYS* 3.8 41.7 - - + -
1164A CYS* 4.6 4.7 - - - -
1171A LEU 3.7 15.3 - - - +
1172A LEU* 2.9 10.9 + - + +
1174A ILE* 1.3 75.9 - - - +
1176A ASN* 1.3 60.5 + - - +
1178A TYR* 3.3 5.1 + - + +
1179A GLU* 2.9 29.0 + - - +
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Residues in contact with ASN1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A LYS* 4.6 11.4 + - - +
1172A LEU* 3.2 29.4 + - - +
1173A LYS* 3.2 14.5 + - + +
1175A ILE* 1.3 75.7 - - - +
1177A ASP* 1.3 62.5 + - - +
1179A GLU* 3.1 16.1 + - - +
1180A GLU* 2.8 31.8 + - - +
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Residues in contact with ASP1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173A LYS* 2.9 51.1 + - - +
1174A ILE* 4.0 6.8 - - - +
1175A ILE 3.3 0.2 - - - -
1176A ASN* 1.3 81.5 - - - +
1178A TYR* 1.3 62.0 + - - +
1180A GLU* 3.3 22.2 + - - +
1181A PHE* 3.5 22.5 - - + -
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Residues in contact with TYR1178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A ALA* 3.8 27.6 - - + -
1101A TYR* 3.6 36.7 - + + +
1104A MET* 3.9 33.7 - - + -
1154A GLU* 3.2 26.8 + - - +
1157A LEU* 4.3 18.8 - - + -
1174A ILE 3.3 11.9 + - - +
1175A ILE* 3.3 10.3 + - - +
1177A ASP* 1.3 79.4 - - - +
1179A GLU* 1.3 62.9 + - + +
1181A PHE* 3.1 36.6 + + + +
1182A SER* 4.9 4.3 + - - -
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Residues in contact with GLU1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157A LEU* 4.2 18.2 - - + +
1161A LYS* 3.3 34.8 + - - +
1175A ILE* 2.9 19.1 + - - +
1176A ASN* 3.1 12.7 + - - +
1178A TYR* 1.3 83.9 - - + +
1180A GLU* 1.3 58.6 + - - +
1181A PHE 3.3 1.7 + - - -
1182A SER* 4.9 6.3 + - - -
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Residues in contact with GLU1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176A ASN* 2.8 12.3 + - - +
1177A ASP* 3.4 18.0 - - - +
1178A TYR 3.1 0.6 - - - -
1179A GLU* 1.3 77.8 - - - +
1181A PHE* 1.3 73.4 + - + +
1182A SER 3.7 4.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il